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The remarkable intraflagellar transport for Flagellum assembly

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The remarkable intraflagellar transport for Flagellum assembly

http://reasonandscience.heavenforum.org/t2642-the-remarkable-intraflagellar-transport-for-flagellum-assembly

The trafficking of bacterial type rhodopsins into the Chlamydomonas eyespot and flagella is IFT mediated 1

500 proteins required for the Flagellum assembly through intracellular highways !

http://reasonandscience.heavenforum.org/t2642-the-remarkable-intraflagellar-transport-for-flagellum-assembly

The Type three secretion system T3SS has over 25 proteins, the flagellum has over 60 proteins. The assembly of the flagellum, however, is a huge commitment for the cell, as this requires the correct production and assembly of more than 500 proteins !! Intraflagellar transport ( IFT ) is a highly orchestrated and dedicated means of protein transport in the cilia/flagella. Both in time (right moment of the cell cycle) and in space (in a defined compartment). Since the flagellum does not possess any ribosomes, all the components needed for its construction must first be synthesized in the cytoplasm and then imported into the flagellum before reaching the distal tip either by transport or by diffusion. In 1993, an active transport of ‘rafts’ was discovered within the flagellum of Chlamydomonas and termed intraflagellar transport (IFT) IFT plays a key role in the construction of the flagellum as its inactivation blocks flagellum formation in all species studied so far.

If we consider not only the proteins to make the flagellum per se, but also all proteins required to assemble it, it seems Charly is just a little more unhappy now !!

Here we present the first report for the existence of an intraflagellar transport (IFT)-interactome mediated trafficking of the bacterial type rhodopsins into eyespot and flagella of the Chlamydomonas. IFT is a highly orchestrated and dedicated means of protein transport in the cilia/flagella11  The assembly, maintenance and functioning of these sensory organelles require IFT. In IFT, large protein complexes called IFT trains move bi-directionally, i.e., from the ciliary base towards the tip (microtubule plus end) of the cilia (anterograde) and backward (retrograde). Anterograde and retrograde movements are powered by the molecular motor proteins, kinesin-2 and cytoplasmic dyneins respectively. These motor proteins in association with IFT particles, carry some of the ciliary cargoes but some ciliary cargoes are known to be carried independently of these motor proteins 2 IFT particles have at least 22 subunits and are composed of sub-complexes IFTA (~6 subunits) and IFTB (~16 subunits) This report provides the first evidence for the involvement of intraflagellar transport (IFT) in the ferrying of bacterial type rhodopsin proteins. IFT molecular motors and IFT particles were found to be involved in the trafficking of Channelrhodopsin ChR1 into the flagella, in a light-dependent manner. The interaction studies provided the evidences of the interaction between Chlamydomonas rhodopsins and the components of IFT machinery along with the proteins involved in the IFT-cargo complex formation. Our data leads to a model in which IFT machinery participates in the rhodopsin transport in unicellular eukaryotic green algae Chlamydomonas reinhardtii. It suggests that IFT mediated trafficking of rhodopsin is not only restricted to vertebrates but also occurs in lower eukaryotes.



Construction of the flagellum: a 500-piece jigsaw 2
The assembly of the flagellum is a huge commitment for the cell, as this requires the correct production and assembly of more than 500 proteins , both in time (right moment of the cell cycle) and in space (in a defined compartment). Assembly of the axoneme  and also of the PFR  takes place at the distal end of the growing flagellum. Since the flagellum does not possess any ribosomes, all the components needed for its construction must first be synthesized in the cytoplasm and then imported into the flagellum before reaching the distal tip either by transport or by diffusion. In 1993, an active transport of ‘rafts’ was discovered within the flagellum of Chlamydomonas and termed intraflagellar transport (IFT) IFT plays a key role in the construction of the flagellum as its inactivation blocks flagellum formation in all species studied so far.

Two distinct complexes (A and B) were identified: the IFT-A complex is a 550-kDa tetramer containing at least five subunits of 144, 140, 139, 122, and 43 kDa, whereas IFT-B complex is a 750-kDa complex containing at least 11 subunits ranging from 20 to 172 kDa (Table 1




Proteins have been grouped according to their category.
When inhibition of a given gene blocked flagellum formation, it was described as an anterograde phenotype (A) and when it stopped retrograde transport, resulting in the formation of shorter flagella filled with IFT material, it was described as a retrograde phenotype (R). Ambiguous phenotypes are shown with a question mark and a hyphen indicates that the gene is conserved but has not been studied in that organism. A cross indicates that the gene is missing from the genome. Experiments were carried out by RNAi knockdown except where indicated. The asterisk denotes an insertion mutant whereas names of the mutant gene obtained by forward genetics are shown in italics

IFT plays a key role in the construction of the flagellum as its inactivation blocks flagellum formation in all species studied so far. Inactivation of any single IFT gene is sufficient to inhibit flagellum assembly, indicating that the integrity of the particle is required for efficient IFT.
The remarkable intraflagellar transport for Flagellum assembly

Figure 3
Canonical model for IFT. 
Step 1: IFT-A and IFT-B complexes, kinesin-2, and inactive cDynein1b gather at the base of the flagellum. 
Step 2: the active kinesin-2 transport IFT-A and IFT-B complexes, inactive cytoplasmic dynein 2, and axonemal precursors from the base to the tip. 
Step 3: kinesin-2 reaches the distal end, where axonemal cargo proteins and IFT particles are released into the ciliary tip compartment. IFT-A and IFT-B complexes dissociate from each other. Complex A binds to active cytoplasmic dynein 2. 
Step 4: active cytoplasmic dynein 2 transports complexes IFT-A and IFT-B and kinesin to the cell body. IFT, intraflagellar transport.

The currently accepted model for IFT mostly relies on studies of Chlamydomonas and is summarized in Figure 3. First, IFT-A and IFT-B complexes, kinesin-2, cytoplasmic dynein 2, and axonemal precursors are produced in the cytoplasm and gather at the flagellum base. Second, once inside the flagellum, the active kinesin-2 transports IFT-A and IFT-B complexes, inactive IFT dynein, and axonemal precursors from the base of the flagellum to the tip. Third, kinesin-2 reaches the distal end of the B microtubule, where axonemal cargo proteins and IFT particles are released into the ciliary tip compartment. Following remodeling of the IFT train, complex A binds to the active IFT dynein. Fourth, the IFT-B complex associates with the IFT-A complex, and the active IFT dynein transports all components, including kinesin-2 back from the tip to the cell body. The IFT cycle is completed when IFT components are returned at the base of the flagellum, where they can be recycled or targeted for destruction.

Flagellar proteins synthesized in the cell body are carried to the tip of the flagellum (the site of assembly of the axoneme) by IFT particles, which are composed of at least 17 highly conserved proteins that form A and B complexes.  The plus end-directed microtubule motor protein kinesin II is essential for movement of particles and their cargo toward the tip (anterograde transport) of the flagellum, and a cytoplasmic dynein carries IFT particles back to the cell body (retrograde transport).  Thus, IFT particles function as constantly moving molecular trucks on a closed loop.  The tracks they travel on are the microtubule doublets of the ciliary/flagellar axoneme, microtubule motors power them, and the individual structural components (e.g., microtubule subunits, dynein arms, and radial spoke proteins) of the cilium/flagellum are their cargo.  4

New proteomic and genomic studies may finally provide a platform for discovery of most of the as yet unidentified genes that encode ciliary/flagellar proteins.  A proteomic analysis of the axoneme of human cilia identified over 200 potentially axonemal proteins (Ostrowski et al., 2002).  Several of the proteins were previously identified as being in the axoneme, but many have no homologs or are of unknown function. 5

(That would be over 200 different kinds of pieces, kids, and a lot of each.)  From genomic studies, they estimate it would require at least 362 genes to build a motionless cilium, and “more than 400-500 genes that are predicted to be needed for forming and regulating the ciliary apparatus”  One team measured the proteome (set of proteins) required to build the basal body (the bottom foundation of the structure) and flagellum to consist of 688 genes.  “There is no doubt,” they say, “that the FABB [flagellar and basal body] proteome represents an incredibly rich resource.” 

Setting-up the scene


Producing at least 500 proteins at about the same time and same place is a sophisticated feat of engineering. This includes proteins constituting the basal body, the transition zone, the IFT particles, and the axoneme (and the PFR in trypanosomatids), as well as membrane elements.Construction of the flagellum follows a strict hierarchy: maturation of the basal body, docking to the membrane, formation of the transition zone, and then elongation of the axoneme.

The switch
Observations in live cells revealed that once trains arrive at the tip of the flagellum, they are rapidly recycled into retrograde trains. Little or no accumulation of IFT material has been reported at the tip.  IFT proteins spend on average 3 to 4 seconds at the tip. 

The inbound journey
The motor that powers retrograde IFT is called cytoplasmic dynein 2 or IFT dynein. This motor complex consists of at least four different subunits. [/size]


- a heavy chain (DHC1B/DHC2) that belongs to the AAA + family of ATPases,
- a light intermediate chain (DYNC2LI1/LIC/XBX1),
- a light chain (LC8), and
- a recently identified putative intermediate chain (IC/FAP133) containing WD repeats

How to deal with bidirectional transport?
IFT is a bidirectional movement of fairly large protein complexes in the narrow space between the microtubules and the flagellum membrane. The visualization of IFT in  Chlamydomonas with fusion GFPs has shown the absence of visible collisions between anterograde and retrograde trains. A simple explanation would be to consider that nine microtubule doublets are available for trafficking and that there is enough room for trains to cross, despite the high frequency of anterograde and retrograde events. An alternative hypothesis consists of using specific and distinct sets of microtubule for anterograde and retrograde trains, exactly as in a train system where outbound and inbound trains use their own tracks. Some doublets serve as specific tracks for anterograde or retrograde transport, hence reducing the risk of collision and offering the opportunity for precise and specific regulation of each set of motor.

In  Current Biology1, three New York geneticists describe the failures that ensue from a mutation in one protein in the IFT family: “kidney cysts, photoreceptor degeneration, skeletal abnormalities, and spermatogenesis defects. ... A targeted Tg737 knockout [to a particular IFT protein] is embryonic lethal, with early embryonic defects that include randomized left/right asymmetry, a consequence of missing cilia on the embryonic ventral node.”  IFT proteins might also be essential for coordinating signals from cilia to other parts of the cell.Like most scientific papers, this one is focused on just one narrow aspect of one protein in one organism, the fruit fly.  As background information, however, they describe what IFT does and how it works.  IFT stands for intraflagellar transport.  It is a family of proteins involved in building the insides of flagella and cilia.  (These are the whip-like appendages common in most living things, from the outboard motors on bacteria, to the sweepers lining your respiratory tract, to the paddling tails on sperm cells).  If you could shrink yourself down to a few microns and watch, here’s what you might see going on inside the shaft of a cilium or flagellum under construction (emphasis added): 3

The eukaryotic cilium or flagellum is a distinct subcellular compartment, with its own characteristic microtubular cytoskeleton, the axoneme, and a membrane that, though continuous with the plasma membrane, can localize distinct sets of proteins.  This distinction is maintained by a specific mechanism of intraflagellar transport (IFT).  IFT was first observed in the single-celled alga Chlamydomonas as a bidirectional movement of uniformly sized particles along the flagellum, in the space between the axoneme and the flagellar membrane.  Biochemical characterization of the particles revealed over 16 constituent proteins associated in A and B subcomplexes.  Particle movement toward the plus ends of the axonemal microtubules at the tip of the flagellum is driven by kinesin II, and mutants lacking kinesin II subunits or complex B proteins do not extend cilia beyond the transition zone of the basal body.  In mutants that express a temperature-sensitive kinesin, flagella shrink after a shift to the restrictive temperature, and this shrinkage indicates that IFT is needed to maintain and regulate flagellar length.  IFT particles and kinesin are returned to the cell body by a nonaxonemal dynein, and mutants with defects in this process typically have swollen cilia that accumulate IFT particles.  Some IFT proteins are concentrated in the cytoplasm close to the basal bodies as well as in the cilia proper, and the transition fibers that connect the basal body to the cell membrane are a possible site for the docking and exchange of IFT particles, motors, and cargo.


In other words, there is a specialized molecular highway down the shaft of a flagellum, between the membranes, with little molecular trucks (dynein and kinesin) that transport cargo (the protein particles) to and from the tips of the growing end.  Intraflagellar transport might be termed the Transportation Department for these organelles.  Since everything from eyes, sperm, and lungs depend on cilia or flagella, you can imagine what happens when a mutation shuts down the highway department and brings construction of these essential organelles to a halt.A related paper in the same issue2 discusses what happens when another one of the IFT proteins, Kinesin II-mediated anterograde intraflagellar transport, mutates and prevents the kinesin truck from moving down the highway.  It makes their cilia sluggish and uncoordinated, and causes auditory defects.An analysis by George Witman (U. of Mass. Medical School) of these papers was published in the subsequent (Oct. 14) issue of Current Biology.3

1Han, Kwok and Kernan, “Intraflagellar Transport Is Required in Drosophila to Differentiate Sensory Cilia but Not Sperm,” Current Biology Vol 13, 1679-1686, 30 September 2003, pp. 1679-1686.
2Sarpal et al., “Drosophila KAP Interacts with the Kinesin II Motor Subunit KLP64D to Assemble Chordotonal Sensory Cilia, but Not Sperm Tails,” Current Biology Vol 13, 1687-1696, 30 September 2003, pp. 1679-1686.
3George B. Witman, “Cell Motility: Deaf Drosophila keep the beat,” Current Biology Vol 13, R796-R798, 14 October 2003.


The authors do not attempt to explain how this system evolved, other than to note that these proteins are highly conserved.  Their paper focuses on one IFT gene in one species, the fruit fly, and the conclusion is that while fruit fly cilia depend on the particular IFT under consideration, their sperm do not.  Surprisingly, fruit fly sperm tails are extremely long, longer than the fly itself, and they are able to grow by other means than IFT, possibly by external supply of components from the cytoplasmStill, think about the problem of pleiotropy for evolution.  It is simplistic to expect one mutation to have only one effect.  As shown here, a mutation, even if beneficial for one part (by some stretch of the imagination), is likely to damage another part, or many other parts.  Shutting down the trucking industry might reduce our dependence on foreign oil, but how will the mail get delivered?  

How will freight get to manufacturers, and finished products get to retailers? In a commonly-cited evolutionary example, a mutation can provide some resistance to malaria, but at the cost of rendering its host vulnerable to a deadly disease: sickle-cell anemia.  Is this all that evolution can hope for?  How can evolutionists really believe that such mistakes led to the high degree of specialization and interrelationship observed in living cells?  Surprisingly, they turn the argument around.  They say that pleiotropy is their ally.  An accident in a gene might lead to major changes all at once.  This is like believing a cosmic ray hit a reptile egg and a bird hatched out. Life, whether in a fruit fly, nematode, alga, or human, involves tightly-knit, coordinated parts.  Every week, it seems, biochemists find some gene or protein that is absolutely essential.  Any mistake either causes major problems, or the organism does not even survive to birth.  Moreover, organisms have complex emergency teams that fight against mutations.  If terrorism doesn’t build a city, don’t expect pleiotropic mutations to evolve life.

Warning: Do NOT Mutate This Protein Complex   06/30/2009     
June 30, 2009 — In each cell of your body there is a complex of 8 or more proteins bound together called the BBSome.  This protein complex, discovered in 2007, should not be disturbed.  Here’s what happens when it mutates: “A homozygous mutation in any BBSome subunit (except BBIP10) will make you blind, obese and deaf, will obliterate your sense of smell, will make you grow extra digits and toes and cause your kidneys to fail.”Children born with Bardet-Beidl syndrome (1 in 100,000 live births) have mutations to one of 14 proteins in this class (and others remain to be identified).  How can one mutation affect so many diverse functions?  Scientists believe that the BBSome is a key component of protein trafficking to the primary cilium, reported Hua Jin and Maxense V. Nachury in Current Biology.1  Primary cilia, they said, are “microtubule-based projections found on many cell types that act like tiny antennae receiving signaling inputs for the cell.”  Functions like sight, smell, and limb patterning rely on signals from primary cilia.  Scientists theorize that the BBSome is involved in providing parts to the intraflagellar transport system (IFT), which delivers construction parts from the base of the cilium or flagellum to the tip.The authors said that the BBSome is “highly conserved” (i.e., unevolved) in all ciliated organisms from single-celled green algae to humans, though absent in plants and fungi.  “This pattern of conservation is a signature for proteins that perform fundamental functions in primary cilium assembly,” they explained.  Only chordates have an additional four BBS proteins. The activity of the BBSome is an ongoing area of research.  When asked what remains to be explored about it, the authors responded, “Nearly everything!”

1.  Hua Jin and Maxense V. Nachury, “Quick Guide: The BBSome,” Current Biology, Volume 19, Issue 12, 23 June 2009, Pages R472-R473.

This story underscores the precision and specificity of proteins.  The sequence of amino acids that leads to a protein’s folded shape is absolutely critical to its function.  Proteins are often hundreds of amino acid links long.  The authors said that mutations to even one of the eight members of the BBSome complex result in death or severe disability.  If the origin of one protein is beyond the reach of chance (see online book), how much more a complex of 8 or more proteins working together?  This does to chemical evolution theory what another H-bomb would do after global nuclear devastation: it just makes the rubble bounce. The answer evolutionists give that some genes are “highly conserved” because they “perform fundamental functions” is a form of the dodge explanation that says, in effect, “if it were not that way, we wouldn’t be here” (see next entry commentary).  It fails to explain where the design came from.  If the origin of a complex system is beyond the reach of chance, what are the alternatives?  Natural law or design.  Natural law, however, produces predictable, repetitive patterns on a simple level – not complex specified information.  That leaves design as the most plausible explanation. 

1. https://www.researchgate.net/publication/308878537_The_trafficking_of_bacterial_type_rhodopsins_into_the_Chlamydomonas_eyespot_and_flagella_is_IFT_mediated
2. https://ciliajournal.biomedcentral.com/articles/10.1186/2046-2530-2-16
3. http://www.creationsafaris.com/crev1003.htm
4. https://sci-hub.bz/http://www.sciencedirect.com/science/article/pii/S0092867404005355
5. http://creationsafaris.com/crev200406.htm

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